10. EPMO Open Source Coordination Office Redaction File Detail Report

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10.1 Files compared

#	Location	File	Last Modified
1	GenISIS_Build_4.zip\Build 4	Genisis2_VIP_Build 4_Deployment_Guide_09152017.docx	Tue Aug 29 18:23:28 2017 UTC
2	GenISIS_Build_4.zip\Build 4	Genisis2_VIP_Build 4_Deployment_Guide_09152017.docx	Wed Oct 4 14:23:15 2017 UTC

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	1	Deployment Guide
	2
	3	Genomic In formation System for Integrate d Science 2
	4	(Genisis2) Technical Services
	5	Release 3
	6
	7
	8	June 2017
	9	Document V ersion 2.0
	10	Department of Vetera ns Affairs
	11
	12
	13	Document R evision Hi story
	14	Date
	15	Revision
	16	Descriptio n
	17	Author
	18	02/10/2017
	19	1.0
	20	Release 1
	21	Booz Allen Hamilton
	22	05/12/2017
	23	2.0
	24	Release 2
	25	Booz Allen Hamilton
	26	06/16/2017
	27	3.0
	28	Release 3
	29	Booz Allen Hamilton
	30
	31	Table of C ontents
	32	1.Introduc tion1
	33	2.Genisis2 Web Appli cation Ser ver Setup2
	34	2.1.1.Setu p the Proj ect on Rem ote Server (VA Envir onment)2
	35	3.Genisis2 Services Server Set up4
	36	3.1.1.Prox y Apache S erver Setu p4
	37	3.1.2.Wild fly Applic ation Serv er Setup6
	38	4.Database Setup6
	39	4.1.1.Data base Names 6
	40	4.1.2.Data base Schem a6
	41	4.1.3.List of Tables within th e Database 7
	42	4.1.4.User s Recogniz ed by the Database7
	43	4.1.5.Data base Scrip ts7
	44	5.Data Ope rations Se tup8
	45	5.1.1.How the Table Copy Proce ss Works8
	46	5.1.2.Sett ing up Lin ux Environ ment8
	47	5.1.3.Sett ing up Win dows SQL S erver Mana gement Ser ver8
	48	5.1.4.Sett ing up the Source Se rver9
	49	5.1.5.Sett ing up the Destinati on Server1 0
	50	5.1.6.Test Reachabil ity Betwee n Servers1 0
	51
	52
	53	Introducti on
	54	The Genisi s2 Deploym ent Guide describes in detail how to ins tall Genis is2 applic ations in the SQA, P rePROD, an d PROD env ironments. The Genis is2 Applic ation Arch itecture i s shown in Figure 1.
	55
	56	VA Intrane t
	57	VA Intrane t
	58
	59
	60
	61
	62
	63	Figure 1: Genisis2 A pplication Architect ure
	64	In order t o proceed with the i nstallatio n, the two Red Hat L inux serve rs should have the f ollowing i nstalled o r at least have perm issions to install:
	65	Apache Web server
	66	Open SSL
	67	SSL certif icates tha t needs to be instal led on two Apache (A ngular and Proxy) se rvers
	68	Wildfly 10 .0.0-Final Applicati on Server
	69	JDK 1.8.0_ 92 or abov e
	70	Other arti facts that are requi red to pro ceed with this insta llation ar e as follo ws:
	71	Environmen t Properti es files:
	72	env.js for Angular w eb applica tion
	73	genisis2.p roperties for Servic es applica tion
	74	Applicatio n Help zip file
	75	Angular ap plication Release zi p artifact
	76	Services a pplication Release w ar artifac t
	77	Database S cripts Rel ease Zip a rtifact
	78	dataTableC opy.sh she ll script file
	79
	80	Genisis2 W eb Applica tion Serve r Setup



	81	Setup the Project on Remote Se rver (VA E nvironment )
	82	Assuming V A Linux bo xes are Re d Hat, the n follow t his instru ction. If you were p rovisioned a separat e server w ith anothe r operatin g system, follow up with your System Adm inistrator .
	83	System Lev el Require ments:
	84	$ sudo yum update
	85	$ sudo yum search ht tpd
	86	Select the correct h ttpd distr o provided by VA RPM repositor y
	87	$ sudo yum install h ttpd.<vers ion>
	88	If it alre ady states installed , ignore a nd move on .
	89	Configure HTTPD:
	90	Make sure /var/www i s owned by root and assigned c orrect pri vileges
	91	chown -Rf root:apach e /var/www
	92	Create dir ectory for the Angul arJS web a pplication
	93	mkdir /var /www/ DNS
	94	mkdir /var /www/ DNS /webroot
	95	mkdir /var /www/ DNS /logs
	96	chown -Rf root:apach e /var/www / DNS
	97	Set permis sions chmo d -Rf 775 /var/www
	98	Copy Angul arJS Appli cation to /var/www/ DNS /webroot
	99	Make sure /var/www/ DNS /webroot/h elp/env.js is presen t
	100	Make sure the json k ey value f or keyname ‘apiURL’ is populat ed with th e url for the wildfl y applicat ion server .
	101	Request an d Install DNS SSL Certi ficates
	102	Make sure private ke y is place d in /etc/ pki/privat e/ DNS .key
	103	Make sure certificat e is place d in /etc/ pki/certs/ DNS .crt
	104	Retrieve r oot certif icate bund le and ins tall
	105	/etc/pki/t ls/certs/c a-bundle.c rt
	106	Setup Apac he for dom ain
	107	Edit /etc/ httpd/conf .d/vhosts. conf as Fo llows:
	108	<VirtualHo st *:80>
	109	Re writeEngin e on
	110	Re writeCond %{SERVER_P ORT} !^443 $
	111	Re writeRule ^/(.*) htt ps://%{HTT P_HOST}/$1 [NC,R=301 ,L]
	112	</Virtual Host>
	113
	114
	115	NameVirtua lHost *:44 3
	116	<VirtualHo st *:443>
	117	ServerAdmi n PII
	118	DocumentRo ot /var/www/ DNS /webroot
	119	ServerName DNS
	120	ServerAlia s www. DNS
	121	ErrorLog /var/www/ DNS /logs/ DNS _error_log
	122	CustomLog /var/www/ DNS /logs/ DNS _access_lo g common
	123	CustomLog /var/www/ DNS /logs/ DNS _ssl_reque st_log "%t %h %{S SL_PROTOCO L}x %{SSL_ CIPHER}x % {SSL_CLIEN T_S_DN}x \ "%r\" %b"
	124
	125	# activate HTTPS on the revers e proxy
	126	SS LEngine On
	127	SSLCertifi cateFile /etc/pki/t ls/certs/ DNS .crt
	128	SSLCertifi cateKeyFil e /etc/pki /tls/priva te/ DNS .key
	129	SS LProtocol -all +TLSv 1 +TLSv1.1 +TLSv1.2
	130	SS LCipherSui te EECDH+A ESGCM:EDH+ AESGCM:AES 256+EECDH: ECDHE- RSA -AES128-SH A:DHE-RSA- AES128-GCM -SHA256:AE S256+EDH:E CDHE-RSA-A ES256-GCM- SHA384:ECD HE-RSA-AES 128-GCM-SH A256:DHE-R SA-AES256- GC$
	131
	132	# activate t he client certificat e authenti cation
	133	SS LCACertifi cateFile / etc/pki/tl s/certs/ca -bundle.cr t
	134	SS LVerifyCli ent requir e
	135	SS LVerifyDep th 3
	136
	137	# initia lize the s pecial hea ders to a blank valu e to avoid http head er forgeri es
	138	He ader set S SL_CLIENT_ S_DN ""
	139	He ader set S SL_CLIENT_ I_DN ""
	140	He ader set S SL_SERVER_ S_DN_OU ""
	141	He ader set S SL_CLIENT_ VERIFY ""
	142
	143	<Locati on />
	144	# add all the S SL_* you n eed in the internal web applic ation
	145	Heade r set SSL_ CLIENT_S_D N "%{SSL_C LIENT_S_DN }s"
	146	Heade r set SSL_ CLIENT_I_D N "%{SSL_C LIENT_I_DN }s"
	147	Heade r set SSL_ SERVER_S_D N_OU "%{SS L_SERVER_S _DN_OU}s"
	148	Heade r set SSL_ CLIENT_VER IFY "%{SSL _CLIENT_VE RIFY}s"
	149	</Locat ion>
	150
	151	</VirtualH ost>
	152
	153	Installing Genisis2W EB:
	154	Get the ap propriate release ve rsions fro m the dev team for t his releas e.
	155	Go to the url: http: //genisis2 0-nexus.bo ozallencsn .com/nexus /
	156	Click on l ogin on to p right si de and ent er followi ng credent ials
	157	Username: Jenkins
	158	Password: root2017
	159	Then go to the follo wing url: http://gen isis20-nex us.boozall encsn.com/ nexus/cont ent/reposi tories/
	160	Be sure to be off of VA VPN. T he above l ink will n ot work in VA VPN.
	161	SFTP Relea se version to Server , in any m eans acces sible by y ou. SFTP w ill direct to /home/ <user>/ - so from th ere unzip the file.
	162	$ unzip <G enisis2Web Zip> /var /www/ DNS /webroot
	163	$ sudo mkd ir help
	164	SFTP help. zip file t o Server, in any mea ns accessi ble by you . . SFTP w ill direct to /home/ <user>/ - so from th ere unzip the file.
	165	$ unzip <G enisis2Web Help Zip> /var/www/ DNS /webroot/h elp
	166	Copy env.j s file pro vided unde r /var/www / DNS /webroot/h elp
	167	Restart Ap ache (serv ice httpd restart)
	168
	169	Genisis2 S ervices Se rver Setup
	170	There are two severs that need to be set up. One is Apache, w hich redir ects all t he request s to Wildf ly Applica tion Serve r.


	171	Proxy Apac he Server Setup
	172	Make sure /var/www i s owned by root and assigned c orrect pri vileges
	173	Chown -Rf root:apach e /var/www
	174	Create dir ectory for the Proxy web appli cation
	175	mkdir /var /www/ DNS
	176	mkdir /var /www/ DNS /webroot
	177	Mkdir /var /www/ DNS /logs
	178	Chown -Rf root:apach e /var/www / DNS
	179	Set permis sions chmo d -Rf 775 /var/www
	180	Copy Proxy Applicati on to /var /www/ DNS /webroot
	181	Request an d Install DNS SSL Certi ficates.
	182	Make sure private ke y is place d in /etc/ pki/privat e/ DNS .key
	183	Make sure certificat e is place d in /etc/ pki/certs/ DNS .crt
	184	Setup Apac he for dom ain Proxy
	185	Edit /etc/ httpd/conf .d/vhosts. conf as Fo llows:
	186	<VirtualHo st *:80>
	187	Re writeEngin e on
	188	Re writeCond %{SERVER_P ORT} !^443 $
	189	Re writeRule ^/(.*) htt ps://%{HTT P_HOST}/$1 [NC,R=301 ,L] </Virt ualHost>
	190
	191	<VirtualHo st *:443>
	192	ServerAdmi n PII
	193	DocumentRo ot /var/www/ DNS /webroot
	194	ServerName DNS
	195	ServerAlia s www. DNS
	196	ErrorLog /var/www/ DNS /logs/ DNS _error_log
	197	CustomLog /var/www/ DNS /logs/ DNS _access_lo g common
	198	CustomLog /var/www/ DNS logs/ DNS ssl_reques t_log "%t %h %{S SL_PROTOCO L}x %{SSL_ CIPHER}x$
	199
	200	# activate H TTPS on th e reverse proxy
	201	SS LEngine On
	202	SSLCertifi cateFile /etc/pki/t ls/certs/ DNS .crt
	203	SSLCertifi cateKeyFil e /etc/pki /tls/priva te/ DNS .key
	204	SS LProtocol -all +TLSv 1 +TLSv1.1 +TLSv1.2
	205	SS LCipherSui te EECDH+A ESGCM:EDH+ AESGCM:AES 256+EECDH: ECDHE-RSA- AES128-SHA :DHE-RSA-A ES128-GCM- SHA256:AES 256+EDH:EC DHE-RSA-AE S256-GCM-S HA384:E$
	206
	207	Pr oxyPass "/ " "http:/ /localhost :8080/"
	208	Pr oxyPass "/ Genisis2Se rvices" "h ttp://loca lhost:8080 /Genisis2S ervices/"
	209	Pr oxyPassRev erse "/Gen isis2Servi ces" "http ://localho st:8080/Ge nisis2Serv ices/"
	210
	211	#W ildfly adm in console access
	212	Pr oxyPass "/ console" " http://loc alhost:999 0/console"
	213	Pr oxyPassRev erse "/con sole" "htt p://localh ost:9990/c onsole"
	214
	215	Pr oxyPass "/ management " "http:// localhost: 9990/manag ement"
	216	Pr oxyPassRev erse "/man agement" " http://127 .0.0.1:999 0/manageme nt"
	217
	218	</VirtualH ost>
	219
	220	Restart Ap ache (serv ice httpd restart)
	221	Wildfly Ap plication Server Set up
	222	Download t he Wildfly applicati on 10.0.0- Final zip file from wildfly.or g/download s
	223	Download a nd install JDK 1.8.0 _92 and in stall it u nder /opt/ JDK_1.8.0_ 92
	224	Set JAVA_H OME variab le to poin t to bin d irectory i n java ins tallation folder
	225	Under /opt directory create wi ldfly dire ctory
	226	mkdir wild fly
	227	Set permis sions chmo d 775 -R / opt/wildfl y
	228	Unzip the downloaded Wildfly z ip file to /opt/wild fly direct ory
	229	You should now see a “standalo ne” direct ory under your wildl fy home
	230	Copy the g ensis2.pro perties un der /opt/w ildfly/sta ndalone/co nfiguratio n director y
	231	Open genis is2.proper ties file using vim and enter correct va lues perta ining to t he environ ment on wh ich the ap plication is being i nstalled
	232	Reach out to the dev elopment t eam for th e correct values to be filled for each p roperty li sted in th e genisis2 .propertie s file
	233	SFTP Relea se version to Server by any me ans access ible by yo u. SFTP wi ll direct to /home/< user>/
	234	Copy the w ar file to /opt/wild fly/standa lone/deplo yments fol der
	235	sudo cp /h ome/<user> / Genisis2 Services.w ar /opt/wi ldfly/stan dalone/dep loyments
	236	Before sta rting the server, ma ke sure th at databas e setup is complete and the pr operty
	237	Start the wildfly se rver
	238	nohup /op t/wildfly/ bin/standa lone.sh &
	239
	240	Database S etup


	241	Database N ames
	242	Genisis_DB is our ap plication database.
	243	Activiti_D B is the a ctiviti wo rkflow dat abase.
	244
	245	Database S chema
	246	The schema used for the applic ation data base is ‘d bo’.
	247
	248	List of Ta bles withi n the Data base
	249	Request Hi story
	250	RequestTyp e
	251	Request
	252	CommentHis tory
	253	StudyAppro val
	254	WorkflowSt atus
	255	Source
	256	Users
	257	User_Role_ Type
	258	User_Appro ver
	259	User_Type
	260	Role_Type
	261	Management Table (We are creat ing the Ma nagement t able only for the ta ble copy f unction. T his behave s as a log for the T able copy process.)
	262	Other syst ems genera ted tables by Activi ti
	263
	264	Users Reco gnized by the Databa se
	265	“genisis” is the app lication u ser in the database with the r ights of d ata reader and data writer wit hin the da tabase.
	266
	267	Database S cripts
	268	Unzip the dbscripts and run th e scripts in the fol lowing ord er:
	269	GENISIS_DB
	270	CreateData base.sql
	271	User.Sql
	272	Tables.Sql
	273	looklookup tables.sql
	274	ACTIVITI_D B
	275	CreateData base.sql
	276	User.Sql
	277
	278	Data Opera tions Setu p


	279	How the Ta ble Copy P rocess Wor ks
	280	There are three serv ers involv ed in tabl e copy pro cess as fo llows:
	281	Management Server – This is th e same as the Genisi s2 Microso ft Windows 2012/ SQL Server 20 12 Databas e server.
	282	Source Ser ver – Micr osoft Wind ows /SQL S erver data base from which tabl es are cop ied (Examp le: VINCI Landing Zo ne server) .
	283	Destinatio n Server – Microsoft Windows/S QL Server to which t ables are copied (Ex ample: Gen isis Landi ng Zone se rver).
	284
	285	Setting up Linux Env ironment
	286	Make sure all the pr operties a re updated in /opt/w ildfly/sta ndalone/co nfiguratio n/genisis2 .propertie s
	287	SFTP Relea se version to Server , in any m eans acces sible by y ou. SFTP w ill direct to /home/ <user>/
	288	Copy the j ar file to /opt/geni sisDataOps folder.
	289	sudo cp /h ome/<user> / Genisis2 DataOps.ja r /opt/gen isisDataOp s/Genisis2 DataOps.ja r
	290	SFTP the s hell scrip t and copy to the /o pt/genisis DataOps fo lder
	291	sudo cp /h ome/<user> / database TableCopy. sh /opt/ge nisisDataO ps/ databa seTableCop y.sh
	292	The table copy proce ss will be initiated from the Genisis2 u ser interf ace. It ex ecutes the above .sh file (she ll script) . In turn, the.jar f ile that p erforms th e table co py process is invoke d.
	293
	294	Setting up Windows S QL Server Management Server
	295	Users and permission s needed
	296	Make sure that Micro soft Windo ws 2012 R2 and SQL s erver 2012 are insta lled in th e Destinat ion and Ma nagement d atabases
	297	Always use Fully qua lified Dom ain Names (FQDNs and not IP ad dresses)
	298	You need a username and passwo rd with th e followin g permissi ons. This is for rou tine Genis is2 initia ted Table Copy Opera tions.
	299	ddlread
	300	ddlwrite
	301	We need to create a linked ser ver in the Source Se rver. For this, you may need a ccess to a username and passwo rd with Ad ministrato r rights f or setting the linke d server u p. This is a one-tim e task.
	302	Creating a Linked Se rver from the Manage ment Serve r (Example : DN S .D NS SQA Sourc e Server t o the (use FQDN not ip) to the Source Se rver (Exam ple: D N S . D NS - VA SQA S ource Serv er) to Lin ked Server :
	303	Login to t he Managem ent server as an Adm inistrator
	304	Create lin ked server in the Ma nagement f or Source Server
	305	Once you s ee the Lin ked Source Server, o pen it and make sure you can s ee the Dat abase you are given access to and the ta bles withi n them. Ru n an auto generated SQL script to see sa y the firs t 1000 row s of a tab le just to make sure that the management server ca n read tha t database and table s within t hat databa se.
	306	Create a L inked Serv er from th e Destinat ion Server to the Ma nagement S erver (For Ex: D NS . URL - VA SQA Destinatio n Server):
	307	Table Copy ing is don e in two s teps
	308	Management Server PU LLS the ta ble from t he Source Server in to a TEMP database ( GENISISTEM PDATA)
	309	Destinatio n Server P ULLS the t able from the Manage ment Serve r (GENISIS TEMPATA) t o the its database ( GENISISDAT AOPSDATA – This is a lso the Ge nisis Land ing Zone D atabase)
	310	You need a username and passwo rd with AD MINISTRATO R rights i n the Dest ination Se rver just for creati ng the Lin ked Server )
	311	Create a L inked Serv er in the Destinatio n Server f or the Man agement Se rver
	312	Once you s ee the Lin ked Manage ment Serve r, open it and make sure you c an see the GENISISTE MPDATA Dat abase
	313	Management Table par t of Genis isDB (Scri pt) (This part is in cluded in the Genisi s2 build a nd this is for refer ence – No tasks to b e done her e)
	314
	315	Setting up the Sourc e Server
	316	The Source Server ca n be a rem ote server like the VINCI land ing Zone. Some other group may be respon sible for administer ing that d atabase. T his step i nvolves co ordination with that group and making su re that th e followin g steps ar e complete d:
	317	Getting an account o n the sour ce server: Coordinat e with the source se rver admin istrative team to ob tain a use r name and password created wi th followi ng permiss ions and t he name of the Datab ase from w hich you w ill be cop ying table s. The per missions n eeded for this datab ase are:
	318	ddlRead
	319	ddlWrite
	320	ddladmin
	321	We are ask ing for th e above pe rmissions; since in the future , this Sou rce Server can serve as a Dest ination Se rver also. You shoul d be able to create a table th ere and wr ite to it.
	322	Setting up the Desti nation Ser ver
	323	Get an acc ount on th e Destinat ion Server with the following permission s:
	324	ddlRead
	325	ddlWrite
	326	ddlAdmin
	327
	328	Test Reach ability Be tween Serv ers
	329	Management Server to Source Se rver:
	330	From a Win dows serve r (within the same s ubnet with permissio ns to acce ss the Des tination S erver) log in to the Management Server us ing SQL Se rver Manag ement Stud io. Determ ine if you can click on linked servers, open them, and see G enisis_DB and the Ma nagement_T able. You need to be able to d o this to verify if tables hav e been cop ied succes sfully, an d the Numb er of Rows and Check sums, BEFO RE, and AF TER a Tabl e Copy. Th is table c ontains th e log for Table Copy Operation s.
	331	Confirm th at you can reach the Source Se rver and l ook at the database given to y ou. Determ ine if the tables ar e there, a nd that yo u are able to run qu eries agai nst this d atabase.
	332	Destinati on Server to Managem ent Server :
	333	From any W indows ser ver, login to the De stination Server usi ng SQL Ser ver Manage ment Studi o. Confirm that you can click on the lin ked server s and open the Manag ement Serv er. Determ ine if you can see t he GENISIS TEMPDATA d atabase. S ince it is a tempora ry databas e where ta bles are s tored temp orarily, y ou may not see any t ables.